IQ-TREE multicore version 1.6.12 for Linux 64-bit built Aug 15 2019
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host:    bell.cibiv.univie.ac.at (AVX2, FMA3, 62 GB RAM)
Command: ../../iqtree -s Cryptopidae_4_genes.raxml -sp Cryptops.partitions.txt -pre Cryptopidae_4_genes.raxml -m TESTNEW -bb 1000 -alrt 1000
Seed:    112247 (Using SPRNG - Scalable Parallel Random Number Generator)
Time:    Mon Nov 17 17:15:59 2025
Kernel:  AVX+FMA - 1 threads (12 CPU cores detected)

HINT: Use -nt option to specify number of threads because your CPU has 12 cores!
HINT: -nt AUTO will automatically determine the best number of threads to use.

Reading partition model file Cryptops.partitions.txt ...
Reading alignment file Cryptopidae_4_genes.raxml ... Phylip format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 39 sequences with 3208 columns, 1037 distinct patterns
734 parsimony-informative, 163 singleton sites, 2311 constant sites
                                            Gap/Ambiguity  Composition  p-value
   1  Scolopocryptops_nipponicus                   10.44%    passed     98.04%
   2  Cormocephalus_aurantiipes                     1.40%    passed     85.83%
   3  Cryptops_anomalans                            5.36%    passed     63.83%
   4  Cryptops_australis                           24.03%    failed      1.29%
   5  Cryptops_doriae                               3.52%    passed     76.87%
   6  Cryptops_galatheae                            0.41%    passed     82.33%
   7  Cryptops_hortensis                            3.80%    passed     50.81%
   8  Cryptops_indicus                              0.34%    passed     98.48%
   9  Cryptops_lamprethus                           3.74%    passed     93.41%
  10  Cryptops_legagus                              3.30%    passed     84.71%
  11  Cryptops_niuensis                             3.93%    passed     56.87%
  12  Cryptops_parisi                               3.49%    passed     62.37%
  13  Cryptops_punicus                             11.44%    passed     13.15%
  14  Cryptops_sarasini                             1.75%    passed     90.88%
  15  Cryptops_spinipes                             4.46%    passed     51.92%
  16  Cryptops_trisulcatus                          1.22%    passed     33.99%
  17  Cryptops_typhloporus                         11.47%    passed     47.34%
  18  Cryptops_weberi                               2.09%    passed     99.88%
  19  Newportia_collaris                            9.85%    passed     19.61%
  20  Newportia_divergens                           3.12%    passed     58.82%
  21  Newportia_ernsti                              1.75%    passed     71.62%
  22  Newportia_longitarsis                         2.52%    passed     66.55%
  23  Newportia_monticola                           4.58%    passed     99.34%
  24  Newportia_quadrimeropus                       0.97%    failed      0.35%
  25  Newportia_stolli                              2.34%    passed     51.45%
  26  Otostigmus_astenus                            1.18%    passed     70.48%
  27  Plutonium_zwierleini                          2.40%    passed     53.88%
  28  Scolopocryptops_macrodon                      9.73%    passed     27.27%
  29  Scolopocryptops_melanostomus_AMNH_LP6249      9.76%    passed     61.44%
  30  Scolopocryptops_melanostomus_MCZ_IZ_130815    9.73%    passed     90.79%
  31  Scolopocryptops_mexicanus_MCZ_IZ_130810       5.14%    passed     99.93%
  32  Scolopocryptops_mexicanus_MCZ_IZ_130812       1.90%    passed     83.17%
  33  Scolopocryptops_miersii                       2.31%    passed     41.67%
  34  Scolopocryptops_nigridius                     1.87%    passed     90.16%
  35  Scolopocryptops_rubiginosus                  11.19%    passed     27.34%
  36  Scolopocryptops_sexspinosus                   5.64%    passed     94.75%
  37  Scolopocryptops_spinicaudus                   3.05%    passed     96.98%
  38  Theatops_erythrocephalus                      2.09%    passed     55.40%
  39  Theatops_posticus                            10.88%    passed     72.22%
****  TOTAL                                         5.08%  2 sequences failed composition chi2 test (p-value<5%; df=3)
NOTE: No CharPartition defined, use all CharSets

Loading 4 partitions...
Subset	Type	Seqs	Sites	Infor	Invar	Model	Name
1		39	369	195	131	TESTNEW	Cryptopidae_16S_mafft_gblocks_fasta
2		39	1814	150	1597	TESTNEW	Cryptopidae_18S_mafft_gblocks_fasta
3		32	255	50	181	TESTNEW	Cryptopidae_28S_mafft_fasta
4		38	770	339	402	TESTNEW	Cryptopidae_COI_mafft_gblocks_fasta
Degree of missing data: 0.020
Info: multi-threading strategy over partitions



Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.007 seconds
NOTE: ModelFinder requires 17 MB RAM!
Testing GTR+F+G on supermatrix...
GTR+F+G4 / LnL: -26094.831 / df: 84 / AIC: 52357.662 / AICc: 52362.234 / BIC: 52867.828
Selecting individual models for 4 charsets using BIC...
 No. Model        Score       Charset
   1 TVM+F+I+G4   11995.973   Cryptopidae_16S_mafft_gblocks_fasta
   2 TNe+R3       12285.200   Cryptopidae_18S_mafft_gblocks_fasta
   3 TNe+R3       3092.064    Cryptopidae_28S_mafft_fasta
WARNING: ABNORMAL_TERMINATION_IN_LNSRCH
   4 GTR+F+I+G4   23257.885   Cryptopidae_COI_mafft_gblocks_fasta
Full partition model BIC score: 51147.054 (LnL: -24301.966  df:315)
Partition information was printed to Cryptopidae_4_genes.raxml.best_scheme.nex
Partition information in Raxml format was printed to Cryptopidae_4_genes.raxml.best_scheme

All model information printed to Cryptopidae_4_genes.raxml.model.gz
CPU time for ModelFinder: 44.688 seconds (0h:0m:44s)
Wall-clock time for ModelFinder: 105.956 seconds (0h:1m:45s)
Generating 1000 samples for ultrafast bootstrap (seed: 112247)...

NOTE: 8 MB RAM (0 GB) is required!
Estimate model parameters (epsilon = 0.100)
Optimizing GTR+F+I+G4 parameters for partition Cryptopidae_COI_mafft_gblocks_fasta (83 free parameters)
Optimizing TNe+R3 parameters for partition Cryptopidae_18S_mafft_gblocks_fasta (81 free parameters)
Optimizing TVM+F+I+G4 parameters for partition Cryptopidae_16S_mafft_gblocks_fasta (84 free parameters)
Optimizing TNe+R3 parameters for partition Cryptopidae_28S_mafft_fasta (67 free parameters)
Optimal log-likelihood: -24326.132

WARNING: Estimated model parameters are at boundary that can cause numerical instability!

Computing ML distances based on estimated model parameters... 0.031 sec
Computing BIONJ tree...
0.001 seconds
Log-likelihood of BIONJ tree: -24318.614
--------------------------------------------------------------------
|             INITIALIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Generating 98 parsimony trees... 2.310 second
Computing log-likelihood of 98 initial trees ... 3.546 seconds
Current best score: -24310.426

Do NNI search on 20 best initial trees
Estimate model parameters (epsilon = 0.100)

WARNING: Estimated model parameters are at boundary that can cause numerical instability!

BETTER TREE FOUND at iteration 1: -24231.390
Estimate model parameters (epsilon = 0.100)

WARNING: Estimated model parameters are at boundary that can cause numerical instability!

UPDATE BEST LOG-LIKELIHOOD: -24230.546
Iteration 10 / LogL: -24230.770 / Time: 0h:0m:35s
Estimate model parameters (epsilon = 0.100)

WARNING: Estimated model parameters are at boundary that can cause numerical instability!

BETTER TREE FOUND at iteration 11: -24229.887
Iteration 20 / LogL: -24231.655 / Time: 0h:0m:38s
Finish initializing candidate tree set (3)
Current best tree score: -24229.887 / CPU time: 13.616
Number of iterations: 20
--------------------------------------------------------------------
|               OPTIMIZING CANDIDATE TREE SET                      |
--------------------------------------------------------------------
Iteration 30 / LogL: -24231.511 / Time: 0h:0m:43s (0h:2m:0s left)
Iteration 40 / LogL: -24231.004 / Time: 0h:0m:46s (0h:1m:24s left)
Iteration 50 / LogL: -24231.006 / Time: 0h:0m:50s (0h:1m:2s left)
Log-likelihood cutoff on original alignment: -24309.012
Iteration 60 / LogL: -24230.664 / Time: 0h:0m:53s (0h:0m:46s left)
Iteration 70 / LogL: -24232.344 / Time: 0h:0m:56s (0h:0m:33s left)
Iteration 80 / LogL: -24231.202 / Time: 0h:1m:0s (0h:0m:23s left)
Iteration 90 / LogL: -24234.177 / Time: 0h:1m:3s (0h:0m:15s left)
Iteration 100 / LogL: -24230.032 / Time: 0h:1m:6s (0h:0m:7s left)
Log-likelihood cutoff on original alignment: -24309.012
NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.998
Iteration 110 / LogL: -24231.561 / Time: 0h:1m:9s (0h:0m:57s left)
TREE SEARCH COMPLETED AFTER 112 ITERATIONS / Time: 0h:1m:10s

--------------------------------------------------------------------
|                    FINALIZING TREE SEARCH                        |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
Optimizing GTR+F+I+G4 parameters for partition Cryptopidae_COI_mafft_gblocks_fasta (83 free parameters)
Optimizing TNe+R3 parameters for partition Cryptopidae_18S_mafft_gblocks_fasta (81 free parameters)
Optimizing TVM+F+I+G4 parameters for partition Cryptopidae_16S_mafft_gblocks_fasta (84 free parameters)
Optimizing TNe+R3 parameters for partition Cryptopidae_28S_mafft_fasta (67 free parameters)
Optimal log-likelihood: -24229.823

WARNING: Estimated model parameters are at boundary that can cause numerical instability!

BEST SCORE FOUND : -24229.823

Testing tree branches by SH-like aLRT with 1000 replicates...
7.862 sec.
Creating bootstrap support values...
Split supports printed to NEXUS file Cryptopidae_4_genes.raxml.splits.nex
Total tree length: 5.821

Total number of iterations: 112
CPU time used for tree search: 18.474 sec (0h:0m:18s)
Wall-clock time used for tree search: 45.475 sec (0h:0m:45s)
Total CPU time used: 33.175 sec (0h:0m:33s)
Total wall-clock time used: 79.393 sec (0h:1m:19s)

Computing bootstrap consensus tree...
Reading input file Cryptopidae_4_genes.raxml.splits.nex...
39 taxa and 146 splits.
Consensus tree written to Cryptopidae_4_genes.raxml.contree
Reading input trees file Cryptopidae_4_genes.raxml.contree
Log-likelihood of consensus tree: -24230.793

Analysis results written to: 
  IQ-TREE report:                Cryptopidae_4_genes.raxml.iqtree
  Maximum-likelihood tree:       Cryptopidae_4_genes.raxml.treefile
  Likelihood distances:          Cryptopidae_4_genes.raxml.mldist
  Best partitioning scheme:      Cryptopidae_4_genes.raxml.best_scheme.nex
           in RAxML format:      Cryptopidae_4_genes.raxml.best_scheme

Ultrafast bootstrap approximation results written to:
  Split support values:          Cryptopidae_4_genes.raxml.splits.nex
  Consensus tree:                Cryptopidae_4_genes.raxml.contree
  Screen log file:               Cryptopidae_4_genes.raxml.log

Date and Time: Mon Nov 17 17:19:04 2025
